Publications

[H-index = 18, also see on Google Scholar and publicationslist.org ]

Books:

Editorials and other not peer-reviewed articles:

  • Anisimova M. 2014. Joint alignment und phylogeny for large genomic data. Transfer, ZHAW December link

  • Anisimova M. , C. Dessimoz 2014. Preface of Proceedings of GNOME 2014 — Festschrift for Gaston Gonnet. PeerJ PrePrints 2:e426v1 link

  • Anisimova M. 2014. Darwin and Fisher meet at biotech: On the potential of computational molecular evolution in industry. PeerJ PrePrints 2:e427v1 in Proceedings of GNOME 2014 — Festschrift for Gaston Gonnet link

  • Anisimova, M., D. A. Liberles, H. Philippe, J. Provan, T. Pupko, and A. von Haeseler 2013. State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol. Biol. 13:161 link

  • See also an interview in Biome

  • Anisimova, M. 2012. Preface to “Evolutionary genomics: statistical and computational methods” (2 vols), ed. Anisimova, in Meth Mol Biol, Springer link

Research articles and book chapters (all peer-reviewed):

  • Anisimova, M., J. P. Bielawski, Z. Yang 2001. Accuracy and power of the likelihood ratio test to detect adaptive molecular evolution. Mol. Biol. Evol. 18:1585-1592 link

  • Anisimova, M., J. P. Bielawski, Z. Yang 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19:950-958 link

  • Anisimova, M., R. Nielsen, Z. Yang 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164: 1229-1236 link

  • Anisimova, M. and Z. Yang 2004. Molecular evolution of HDV antigen gene: recombination or positive selection? J. Mol. Evol. 59: 815-826 link

  • Balakirev, E.S., M. Anisimova, F.J. Ayala 2006. Positive and negative selection in the beta-esterase gene cluster of the Drosophila melanogaster subgroup. J. Mol. Evol. 62: 496-510 link

  • Anisimova, M. and O. Gascuel. 2006. Approximate likelihood ratio test for branches: a fast, accurate and powerful alternative. Syst. Biol. 55(4):539-552 link

  • Anisimova, M. and Z. Yang 2007. Multiple hypotheses testing to detect adaptive protein evolution affecting individual branches and sites. Mol. Biol. Evol. 24:1219-1228 link

  • Anisimova, M., J.P. Bielawski, K. Dunn, Z. Yang 2007. Phylogenomic analysis of natural selection pressure in Streptococcus. BMC Evol. Biol. 7:154-167 link

  • Anisimova, M. and D. A. Liberles. 2007 The quest for natural selection in the age of comparative genomics. Heredity 99:567-579 link

  • Kajava, A.V., M. Anisimova, N. Peeters 2008. Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: from plants to bacteria? PLoS One 3(2): e1694. link

  • Anisimova, M. and C. Kosiol 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol. Biol. Evol. 26(2):255-271 link

  • Dimitrieva, S. and M. Anisimova 2010. PANDITplus: toward better integration of evolutionary view on molecular sequences with supplementary bioinformatics resources. Trends Evol. Biol. 2(1): e1 link

  • Guindon, S., JF. Dufayard, V. Lefort, M. Anisimova, W. Hordijk and O. Gascuel 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 Syst. Biol. 59(3):307-321 link

  • Anisimova*, M., G.M. Cannarozzi* , D.A. Liberles* 2010. Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends Evol. Biol. 2(1): e7 link

  • Anisimova, M., M. Gil, JF. Dufayard, C. Dessimoz, O. Gascuel 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol 60:685–699; doi: 10.1093/sysbio/syr041 link

  • Schirrmeister B. E., M. Anisimova, A. Antonelli, H. C. Bagheri 2011. Evolution of cyanobacterial morphotypes: taxa required for improved phylogenomic approaches. Communicative & Integrative Biology link

  • Szalkowski A., and M. Anisimova 2011. Markov models of amino acid substitution to study proteins with intrinsically disordered regions. PLoS One 6(5): e20488. doi:10.1371/journal.pone.0020488 link

  • Balakirev E.S., M. Anisimova, F.J. Ayala 2011. Complex interplay of evolutionary forces in the ladybird homeobox genes of Drosophila melanogaster.PLoS One 6(7): e22613. doi:10.1371/journal.pone.0022613 link

  • Remigi P., M. Anisimova, A. Guidot, S. Genin, N. Peeters. 2011. Functional diversification of the GALA type-three effector family contributes to Ralstonia solanacearum adaptation on several plant hosts. New Phytologist DOI: 10.1111/j.1469-8137.2011.03854.x link

  • Dalquen D. A, M. Anisimova, G. Gonnet, and C. Dessimoz 2011. ALF - A simulation framework for genome evolution. Mol Biol Evol doi: 10.1093/molbev/msr268 link

  • Wang M, M. Kapralov, M. Anisimova 2011. Co-evolution of amino acid residues in the key photosynthetic enzyme RuBisCo in land plants. BMC Evol Biol 11:266 link

  • Kosiol C. and M. Anisimova 2012. Methods for detecting natural selection in protein-coding genes in "Evolutionary Genomics: statistical and computational methods" vol. 2 , ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer link

  • Anisimova, M. 2012. Parametric models of codon evolution in Codon Evolution: mechanisms and models, eds. Cannarozzi G, Schneider A., Oxford University Press link

  • Anisimova, M. and D. Liberles 2012. Detecting and understanding natural selection, in Codon Evolution: mechanisms and models, eds. Cannarozzi G, Schneider A., Oxford University Press link

  • Roth, A., M. Anisimova, G.M. Cannarozzi 2012. Measuring codon usage bias, in Codon Evolution: mechanisms and models, eds. Cannarozzi G, Schneider A., Oxford University Press link

  • Schirrmeister, B.E., D.A. Dalquen, M. Anisimova, H.C. Bagheri 2012. Gene copy number variation and its significance in cyanobacterial phylogeny. BMC Microbiology 2:177, doi:10.1186/1471-2180-12-177 link

  • Schaper, E., A.V. Kajava, A. Hauser, M. Anisimova 2012. Repeat or not repeat?—Statistical validation of tandem repeat prediction in genomic sequences Nucl. Acids Res. 40 (20): 10005-10017. link

  • Gil*, M., M.S. Zanetti*, S. Zoller, M Anisimova 2013. CodonPhyML: Fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol 30(6):1270-80 open acsess

  • Szalkowski, A., and M. Anisimova 2013. Graph-based modeling of tandem repeats improves global multiple sequence alignment. Nucl Acids Res doi: 10.1093/nar/gkt628 link

  • Peeters, N., S. Carrère, M. Anisimova, L. Plener, A.C. Cazalé, S. Genin 2013. Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics 14:859, doi:10.1186/1471-2164-14-859 link

  • Schaper, E., O. Gascuel, M. Anisimova 2014. Deep conservation of human protein tandem repeats within the eukaryotes. MolBiol Evol doi: 10.1093/molbev/msu062 link

  • Sidorova, J. and M. Anisimova 2014. NLP-inspired structural pattern recognition in chemical application. Pattern Recognition Letters 45:11–16 link

  • Dimitrieva, S. and M. Anisimova 2014. Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. PLoS ONE 9(6): e95034. doi:10.1371/journal.pone.0095034 link

  • Rech, G.E., J.M. Sanz-Martín, M. Anisimova, S.A. Sukno, M.R. Thon 2014. Natural selection at coding and non-coding DNA mainly affects pathogenicity-related genes in the hemibiotrophic fungus Colletotrichum graminicola. (pending re-review) link

  • Anisimova M. 2014. Darwin and Fisher meet at biotech: On the potential of computational molecular evolution in industry. (submitted for review) Preprint is currently available in PeerJ PrePrints 2:e427v1 in Proceedings of GNOME 2014 — Festschrift for Gaston Gonnet link

  • Schaper, E.and M. Anisimova 2014. The evolution and function of protein tandem repeats in plants. New Phytologist DOI: 10.1111/nph.13184 link

  • Mirsky, A., L. Kazandjian, M. Anisimova 2015. Antibody-specific model of amino acid substitution for immunological inferences from alignments of antibody sequences. Mol Biol Evol in press link

  • Anisimova, M. , J. Pecerska, E. Schaper, 2015. Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Frontiers Bioeng Biotech (to appear) link